Development of a Real-Time PCR Protocol Requiring Minimal Handling for Detection of Vancomycin-Resistant Enterococci with the Fully Automated BD Max System

Adaptation and validation of a quantitative vanA/vanB DNA screening assay on a high-throughput PCR system

Vancomycin resistant enterococci (VRE) are a leading cause of ICU-acquired bloodstream infections in Europe. The bacterial load in enteral colonization may be associated with a higher probability of transmission. Here, we aimed to establish a quantitative vanA/vanB DNA real-time PCR assay on a high-throughput system. Limits of detection (LOD), linear range and precision were determined using serial bacterial dilutions. LOD was 46.9 digital copies (dcp)/ml for vanA and 60.8 dcp/ml for vanB. The assay showed excellent linearity between 4.7 × 101 and 3.5 × 105 dcp/ml (vanA) and 6.7 × 102 and 6.7 × 105 dcp/ml (vanB). Sensitivity was 100% for vanA and vanB, with high positive predictive value (PPV) for vanA (100%), but lower PPV for vanB (34.6%) likely due to the presence of vanB DNA positive anerobic bacteria in rectal swabs. Using the assay on enriched VRE broth vanB PPV increased to 87.2%. Quantification revealed median 2.0 × 104 dcp/ml in PCR positive but VRE culture negative samples and median 9.1 × 104 dcp/ml in VRE culture positive patients (maximum: 107 dcp/ml). The automated vanA/B_UTC assay can be used for vanA/vanB detection and quantification in different diagnostic settings and may support future clinical studies assessing the impact of bacterial load on risk of infection and transmission.

Update on activity of dalbavancin and comparators against clinical isolates of Gram-positive pathogens from Europe and Russia (2017-2018), and on clonal distribution of MRSA

BACKGROUND

Gram-positive pathogens remain a major cause of healthcare- and community-associated infections. In particular, the dissemination of methicillin-resistant staphylococci, as methicillin-resistant S. aureus (MRSA) and vancomycin-resistant enterococci (VRE), have significantly reduced the therapeutic options, making the management of these infections even more challenging. Dalbavancin is a second-generation lipoglycopeptide approved for the treatment of moderate to severe acute bacterial skin and skin structure infections (ABSSSIs) caused by Gram-positive organisms, showing a bactericidal effect and a low propensity towards the selection of resistance over time.

AIM

This study aimed to evaluate the antimicrobial activity of dalbavancin and other comparators against recent clinical isolates of Gram-positive pathogens obtained from different sources and from several European countries, including countries of southern and eastern Europe and Russia, where resistance rates are typically high. This study also aimed to describe the clonal relationship of MRSA strains circulating in southern and eastern Europe and Russia.

RESULTS

A total of 1478 isolates were collected. Study results demonstrated the excellent and stable activity of dalbavancin against Gram-positive microorganisms, including MRSA. Interestingly, dalbavancin has retained unaltered MIC₅₀ and MIC₉₀ values over the years and seemed to have a low propensity in selecting resistance mechanisms.

CONCLUSIONS

Our data supported the potential efficacy of dalbavancin against Gram-positive bacteria and uncommon Gram-positive pathogens in patients with ABSSSIs. Of note, few CoNS isolates were resistant to dalbavancin and susceptible to vancomycin, pointing out the importance of testing the susceptibility to dalbavancin before its administration for CoNS infections.

The Impact of Discontinuing Contact Precautions and Enforcement of Basic Hygiene Measures on Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission

OBJECTIVES

Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a pathogen of major public health concern. Although definitive evidence is lacking, contact precautions have been a crucial element in infection prevention and control (IPC) strategies designed to limit nosocomial VRE transmissions. This study investigates the effect of discontinuing contact precautions while enforcing basic hygiene measures, including hand hygiene, environmental cleaning, and antiseptic body washing, for VRE patients at ICUs on prevention of nosocomial VRE transmission causing bacteraemia.

METHODS

Contact precaution was discontinued in January 2018. A total of 96 VREfm isolates from 61 ICU patients with VREfm bacteraemia and/or colonization from 8 ICUs in 2016 and 2019 in a tertiary care hospital were characterized by whole genome sequenicng. VRE transmission was investigated using patient movement data and admission screening for reliable identification of nosocomial acquisition.

RESULTS

Discontinuation of contact precautions did not increase VREfm transmission events (8 in 2016 vs 1 in 2019). While the rate of endogenous VREfm was similar in both years (38% vs 31%), the number of non-colonized patients prior to VREfm bacteraemia was 16 (16/29; 55%) in 2019, which was significantly higher than in 2016 (8/32; 25%). The mean incidence density for VREfm bacteraemia was similar for both years; 0.26 versus 0.31 per 1000 patient days in 2016 and 2019, respectively.

CONCLUSION

Our data suggest that discontinuation of contact precaution, while enforcing the basic hygiene measures did not lead to an increase of nosocomial bloodstream infection rates due to transmissions of VREfm in hyperendemic ICU settings.

Challenges in interpretation of WGS and epidemiological data to investigate nosocomial transmission of vancomycin-resistant Enterococcus faecium in an endemic region: incorporation of patient movement network and admission screening

OBJECTIVES

VRE are listed, by the WHO, among the leading resistant pathogens causing greatest public concern; hence the spread and transmission of VRE, especially in hospitalized patients, need to be monitored. Despite the advancements in typing methods since the implementation of WGS for outbreak investigations, data interpretation, especially for vancomycin-resistant Enterococcus faecium (VREfm) in an endemic setting, remains challenging. In this study we explored the potential added benefit of incorporating patient movement data and admission screening to accurately estimate the magnitude of an outbreak.

METHODS

We sequenced 73 VREfm isolates from patients with bacteraemia (n = 43) and rectal colonization (n = 30/32). Genetic relatedness was determined by SNP distance (≤10) between isolates. Patient movements were visualized in a movement network, along with contact intensity and rectal colonization status prior to infection onset.

RESULTS

ST117, ST80 and ST203 were the predominant STs in our study population. Forty-four percent (18/41) of VREfm bacteraemia cases were of endogenous origin. SNP analysis of infection and colonization isolates revealed nine clonal groups. Eighty-six percent (37/43) of the patients were visualized in a transmission network due to spatiotemporal overlap. Nineteen out of 43 (44%) belonged to five transmission clusters. Incorporation of prior colonization status revealed that transmission was very likely in only 63% (12/19) of patients in these transmission clusters.

DISCUSSION

Although interpretation of WGS data is challenging, incorporation of patient movement data and colonization status by admission screening of high-risk patients may provide additional resolution when interpreting the magnitude of an outbreak in an endemic setting.

Increasing Cytomegalovirus Detection Rate from Respiratory Tract Specimens by a New Laboratory-Developed Automated Molecular Diagnostic Test

Lots of automated molecular methods for detecting cytomegalovirus (CMV) DNA in the blood are available, but seldom for various clinical specimens. This study was designed to establish a highly sensitive automated assay to detect CMV DNA in non-blood specimens. We designed a new QMT assay using QIAGEN artus CMV RG polymerase chain reaction (Q-CMV PCR) kit applied on the BD MAX system and compared with the other assays, including an RGQ assay (LabTurbo auto-extraction combined Q-CMV PCR kit on Rotor-Gene-Q instrument), and in-house PCR assay. A total of 1067 various clinical samples, including 426 plasma, 293 respiratory tract specimens (RTS), 127 stool, 101 cerebral spinal fluid, 90 vitreous humours were analysed. Examining CMV DNA in simultaneous specimens of the same immunocompromised patient with respiratory symptoms, the detection rate of RTS (93.6%, 88/94) was significant higher than plasma (65.9%, 62/94). The positive rates for plasma samples with a low CMV viral load (<137 IU/mL) and diagnostic sensitivity of QMT, RGQ, and in-house assays were 65% and 99.1%, 45% and 100%, 5% and 65.5%, respectively. The QMT assay performs better, with shorter operational and turnaround time than the other assays, enabling the effective and early detection of CMV infection in various clinical specimens, particularly for RTS.

Shorter Incubation Times for Detecting Multi-drug Resistant Bacteria in Patient Samples: Defining Early Imaging Time Points Using Growth Kinetics and Total Laboratory Automation

Background

The transition from manual processing of patient samples to automated workflows in medical microbiology is challenging. Although automation enables microbiologists to evaluate all samples following the same incubation period, the essential incubation times have yet to be determined. We defined essential incubation times for detecting methicillin-resistant Staphylococcus aureus (MRSA), multi-drug resistant gram-negative bacteria (MDRGN), and vancomycin-resistant enterococci (VRE).

Methods

We monitored the growth kinetics of MRSA, MDRGN, and VRE between two and 48 hours on chromogenic media to establish the time points of first growth, single colony appearance, and typical morphology for 10², 10⁴, 10⁶, and 10⁸ colony forming units/mL. Subsequently, we imaged plates inoculated with 778 patient samples after 20, 24, and 36 hours.

Results

The first growth, single colony appearance, and typical morphology time points were inoculum-dependent. First growth appeared after 6–18 hours, 4–18 hours, and 8–48 hours for MRSA, MDRGN, and VRE, respectively, and single colonies appeared at 12–18 hours, 6–20 hours, and 12–48 hours, respectively. Typical morphology was visible at 14–22 hours and 12–48 hours for MRSA and VRE, but was not determined for MDRGN. By examining patient samples, ≥98% of MRSA and MDRGN were visible 20 hours after the start of incubation. Following 24 hours of incubation, only 79.5% of VRE were clearly visible on the respective plates.

Conclusions

An incubation time of 20 hours is sufficient for detecting MRSA and MDRGN. VRE growth is much slower and requires additional imaging after 36 hours.

Profile of the triplex assay for detection of chlamydia, gonorrhea and trichomonas using the BD MAX™ System

INTRODUCTION

Chlamydia, gonorrhea and trichomonas are the most common curable STI. improved access to testing could reduce infection rates and prevent sequelae. nucleic acid amplification tests are the recommend class of diagnostic assay for these infections which are often asymptomatic. Areas covered: A description of the BD MAX™ System (MAX) and the BD MAX CT/GC/TV assay is provided along with data from a large US clinical trial. The capacity of the system for other tests and for lab developed assays is also described. Expert commentary: The CT/GC/TV assay on the MAX is a triplex PCR assay suitable for use with female urine and vaginal or endocervical swab samples. Male urine can be tested by ordering the CT/GC results but has not yet been evaluated for trichomonas. The assay performance characteristics are similar to those of assays run on high-throughput platforms with sensitivity ≥91.5% and specificity ≥98.6% for all analytes. Screening with the CT/GC/TV assay can be combined with testing for vaginitis which would provide a greater depth of coverage for common co-infections. The throughput is moderate (1-48 samples per 8-hour shift) but the menu includes assays beyond STI pathogens making this a suitable platform for moderate volume laboratories.